This report is generated by the tcge-cfmedip-seq-pipeline
Selected QC metrics
- NOTE: The heatmap is drawn based on transformed Z scores. In
general, the darker, the worse! Specifically:
- raw_reads_depth, usable_reads_depth, saturation_maxEstCor and
enrichment_GoGe: the darker, the lower
- coverage_pctReadsWoCpG and coverage_pctCpGwoRead: the darker, the
higher
- fragment_size_mode: the darker, the further away from the mean
mode
Reads QC metrics
Summary statistics for raw, prefilter and aligned reads
- raw_reads_depth: number of raw reads or read pairs
- prefilter_reads: reads or read pairs after QC, adapter trimming and
UMI barcode extraction (p.r.n)
- mapped_reads_pct: percentage of mapped reads or read pairs over the
prefileter_reads
- usable_reads: reads or read pairs after removing the duplication.
reads pairs require properly paired as well
- usable_reads_pct: percentage of usable reads over raw
reads
Number of samples: 162
| Min |
32262542 |
32254934 |
99.95 |
48.00 |
18.67 |
98.29 |
15034504 |
19.76 |
| Q1 |
58120913 |
58101006 |
99.97 |
50.00 |
46.51 |
99.68 |
31350996 |
50.58 |
| Median |
64330110 |
64311496 |
99.97 |
51.00 |
54.97 |
99.73 |
36831907 |
58.19 |
| Mean |
68967120 |
68949118 |
99.97 |
50.94 |
52.16 |
99.71 |
37615009 |
55.68 |
| Q3 |
75255763 |
75229242 |
99.98 |
52.00 |
60.12 |
99.76 |
43789550 |
64.71 |
| Max |
165019785 |
164978205 |
99.99 |
57.00 |
71.05 |
99.83 |
96641876 |
77.71 |
Usable read depth per sample
Usable read depth percentages against raw read depth per sample
Fragment QC metrics
Fragment size ranges with >=80% properly paired reads
- Calculated by based on PICARD MEDIAN_INSERT_SIZE +
WIDTH_OF_80_PERCENT/2
- WIDTH_OF_80_PERCENT: The “width” of the bins, centered around the
median, that encompass 80% of all read pairs.
MEDIPS QC metrics
Saturation and Coverage Metrics
Number of samples: 162
| Min |
0.9900 |
0.440 |
20.67 |
10.60 |
14.65 |
| Q1 |
1.0000 |
0.860 |
29.84 |
12.60 |
27.12 |
| Median |
1.0000 |
1.060 |
34.27 |
13.33 |
32.05 |
| Mean |
0.9978 |
1.185 |
34.54 |
13.36 |
31.22 |
| Q3 |
1.0000 |
1.377 |
38.72 |
13.96 |
35.48 |
| Max |
1.0000 |
6.030 |
51.94 |
17.82 |
48.14 |
Coverage: percentage of usable reads without CpG, and CpGs without
reads
Enrichment score per sample